Align 3-dehydroquinate dehydratase; 3-dehydroquinase; Type II DHQase; EC 4.2.1.10 (characterized)
to candidate WP_028314075.1 G491_RS0107045 type II 3-dehydroquinate dehydratase
Query= SwissProt::P43877 (154 letters) >NCBI__GCF_000429905.1:WP_028314075.1 Length = 151 Score = 160 bits (405), Expect = 8e-45 Identities = 81/142 (57%), Positives = 104/142 (73%), Gaps = 1/142 (0%) Query: 4 ILLLNGPNLNMLGKREPHIYGSQTLSDIEQHLQQSAQAQGYELDYFQANGEESLINRIHQ 63 IL+LNGPNLNMLGKREP +YGS TL +I + L A+ G E+ FQ+N E +L+ +I + Sbjct: 9 ILVLNGPNLNMLGKREPEVYGSTTLDEINEGLITQAEELGLEVQCFQSNSEGALVTKIQE 68 Query: 64 AFQNTDFIIINPGAFTHTSVAIRDALLAVSIPFIEVHLSNVHAREPFRHHSYLSDVAKGV 123 AFQN D IIINP A+THTSVAIRDALL +P IE+HLSNV+ RE FRH S++S VA Sbjct: 69 AFQNVDGIIINPAAYTHTSVAIRDALLLHDVPIIELHLSNVYKREEFRHKSFVSGVATAQ 128 Query: 124 ICGLGAKGYDYALDFAISELQK 145 + G GA GY+ AL A++++ K Sbjct: 129 MAGFGAMGYNMALQ-AMADMVK 149 Lambda K H 0.320 0.137 0.395 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 75 Number of extensions: 1 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 154 Length of database: 151 Length adjustment: 17 Effective length of query: 137 Effective length of database: 134 Effective search space: 18358 Effective search space used: 18358 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 43 (21.2 bits)
Align candidate WP_028314075.1 G491_RS0107045 (type II 3-dehydroquinate dehydratase)
to HMM TIGR01088 (aroQ: 3-dehydroquinate dehydratase, type II (EC 4.2.1.10))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01088.hmm # target sequence database: /tmp/gapView.22665.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01088 [M=141] Accession: TIGR01088 Description: aroQ: 3-dehydroquinate dehydratase, type II Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-66 208.5 0.3 1.7e-66 208.4 0.3 1.0 1 lcl|NCBI__GCF_000429905.1:WP_028314075.1 G491_RS0107045 type II 3-dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429905.1:WP_028314075.1 G491_RS0107045 type II 3-dehydroquinate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 208.4 0.3 1.7e-66 1.7e-66 2 140 .. 9 147 .. 8 148 .. 0.99 Alignments for each domain: == domain 1 score: 208.4 bits; conditional E-value: 1.7e-66 TIGR01088 2 ilvlnGPnlnlLGkrepkvyGsltleeieelleeaakelevevevfqsnsegelidkihealeqvdgiv 70 ilvlnGPnln+LGkrep+vyGs+tl+ei+e l ++a+el++ev++fqsnseg l++ki+ea+++vdgi+ lcl|NCBI__GCF_000429905.1:WP_028314075.1 9 ILVLNGPNLNMLGKREPEVYGSTTLDEINEGLITQAEELGLEVQCFQSNSEGALVTKIQEAFQNVDGII 77 89******************************************************************* PP TIGR01088 71 inpaalthtsvalrDalaavslPvvevhlsnvhareefrkksvlaevakGvivGlGakgyklalealve 139 inpaa+thtsva+rDal+ +P++e+hlsnv++reefr+ks+++ va+ ++ G+Ga gy++al+a+++ lcl|NCBI__GCF_000429905.1:WP_028314075.1 78 INPAAYTHTSVAIRDALLLHDVPIIELHLSNVYKREEFRHKSFVSGVATAQMAGFGAMGYNMALQAMAD 146 ******************************************************************998 PP TIGR01088 140 a 140 + lcl|NCBI__GCF_000429905.1:WP_028314075.1 147 M 147 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (141 nodes) Target sequences: 1 (151 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 4.60 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory